Program SEQ & CCB

Day 1: Friday, April 10

14:00 - 14:10 Opening Remarks
14:10 - 15:10 KEYNOTE: Marco Gerlinger Structure and dynamics of cancer heterogeneity landscapes: analytical approaches and challenges
15:10 - 15:50 Contributed talks (separate sessions)
Session - SEQ Session - CCB
15 min HIGHLIGHT: Faraz Hach, Ibrahim Numanagic and S. Cenk Sahinalp DeeZ: reference-based compression by local assembly SHORT TALK: Ekta Khurana Computational identification of noncoding cancer drivers from whole-genome sequencing data
20 min PAPER TALK: Yuzhen Ye and Haixu Tang Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis HIGHLIGHT: Hatice U. Osmanbeyoglu, Raphael Pelossof, Jacqueline F. Bromberg, Christina S. Leslie Linking Signaling Pathways to Transcriptional Programs in Breast Cancer
15:50 - 16:20 Coffee break
16:20 - 17:30 Contributed talks (joint session)
15 min SHORT TALK: Norbert Dojer, Abhishek Mitra, Yea-Lih Lin, Anna Kubicka, Magdalena Skrzypczak, Krzysztof Ginalski, Philippe Pasero and Maga Rowicka Computational detection of DNA double-stranded breaks and inferring mechanisms of their formation
20 min PAPER TALK: Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Regnier and Valentina Boeva SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability
15 min SHORT TALK: David Seifert, Francesca Di Giallonardo, Karin J. Metzner, Huldrych F. Günthard and Niko Beerenwinkel A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory
20 min PAPER TALK: Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Chuck Cannon and Fengzhu Sun Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics
17:30 - 18:30 KEYNOTE: Jacek Błażewicz DNA Sequencing - from SBH to NGS and Hybrid Algorithms
20:00 Conference Dinner at the Villa Foksal Restaurant, 3/5 Foksal Street

Day 2: Saturday, April 11

09:00 - 10:00 KEYNOTE: Francesca Ciccarrelli Proliferation history of tumors and impact on therapy
10:00 - 10:30 Coffee break
10:30 - 12:00 Contributed talks (separate sessions)
Session - SEQ Session - CCB
20 min PAPER TALK: Davide Verzotto, Audrey S.M. Teo, Axel Hillmer and Niranjan Nagarajan Index-based map-to-sequence alignment in large eukaryotic genomes HIGHLIGHT: Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Alejandro A. Schäffer, Russell Schwartz Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics
15 min SHORT TALK: Damian Wójtowicz, Fedor Kouzine, Arito Yamane, Craig J. Benham, Rafael C. Casellas, David Levens and Teresa M. Przytycka Genome-wide Mapping and computational analysis of non-B DNA structures in vivo SHORT TALK: Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field and Ben Raphael Reconstruction of clonal trees and tumor composition from multi-sample cancer sequencing data
15 min HIGHLIGHT: Benjamin Buchfink, Chao Xie and Daniel Huson Fast and Sensitive Protein Alignment using DIAMOND SHORT TALK: Amit G. Deshwar, Levi Boyles, Jeff Wintersinger, Paul C. Boutros, Yee Whye Teh, Quaid Morris Resolving ambiguities in tumour phylogenies
20 min PAPER TALK: Birte Kehr, Pall Melsted and Bjarni Halldorsson PopIns: population-scale detection of novel sequence insertions PAPER TALK: Simona Constantinescu, Ewa Szczurek, Pejman Mohammadi, Jörg Rahnenführer and Niko Beerenwinkel A Waiting Time Model for Mutually Exclusive Cancer Alterations
15 min HIGHLIGHT: Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi, Claire Lemaitre and Pierre Peterlongo DiscoSnp: Reference-free detection of isolated SNPs SHORT TALK: Yuichi Shiraishi, Georg Tremmel, Satoru Miyano and Matthew Stephens Extraction of Latent Probabilistic Mutational Signature in Cancer Genomes
12:00 - 13:30 Lunch
13:30 - 14:30 Poster viewing
14:30 - 16:00 Contributed talks (separate sessions)
Session - SEQ Session - CCB
15 min HIGHLIGHT: Nathanael Fillmore, Bo Li, Yongsheng Bai, Mike Collins, James A. Thompson, Ron Stewart and Colin N. Dewey Evaluation of de novo transcriptome assemblies from RNA-Seq data SHORT TALK: Isaac Joseph, Shannon McCurdy, Lior Pachter and Joseph F. Costello A method for combining multiple genomic and clinical datatypes to predict recurrence grade in gliomas
20 min PAPER TALK: Monica Golumbeanu, Pejman Mohammadi and Niko Beerenwinkel Probabilistic modeling of occurring substitutions in PAR-CLIP data SHORT TALK: Teresa Przytycka Integrated analysis of mutual exclusivity and gene interaction in Pan-Cancer dys-regulated pathways
20 min PAPER TALK: Nicolas Bray and Lior Pachter Rank Regularized RNA-seq SHORT TALK: Mathieu Lajoie, Sylvie Langlois, Pascal St-Onge, Patrick Beaulieu, Jasmine Healy and Daniel Sinnett Personalized Targeted Therapy for Refractory Childhood Cancers
15 min SHORT TALK: Aaron Lun and Gordon Smyth Using csaw to detect differentially bound regions in ChIP-seq data SHORT TALK: Ashar Ahmad and Holger Froehlich Dirichlet Process Mixture Model with Bayesian Lasso for consistent clustering of Survival Times with Molecular Data
15 min SHORT TALK: Alessandro Mammana and Ho-Ryun Chung Chromatin segmentation with a joint model for reads explains a larger portion of the epigenome SHORT TALK: Ewa Szczurek, Tyll Krüger, Barbara Klink and Niko Beerenwinkel The bottleneck of metastasis formation: insights from a stochastic model
16:00 - 16:30 Coffee
16:30 - 17:30 KEYNOTE: Gerton Lunter Analytical challenges in next-generation sequencing
17:30 Closing remarks